single-cell RNA-seq of OVCAR3 and CCL218 cancer cells with evolved hydroxychloroquine resistance
Experimental procedures followed established techniques using the Chromium Single Cell 3 Library v3.1 Kit (10x Genomics). Cultured cells in single-cell suspension were labeled with TotalSeq-B anti-human Hashtag antibodies (Biolegend) and pooled in equal proportions prior to loading onto a 10X Genomics Next GEM Chip G and emulsified with 3 Single Cell Next GEM beads using a Chromium Controller (10x Genomics). From barcoded cDNAs, gene expression (GEX) libraries were constructed using Chromium Next GEM Single Cell 3? Library kit and hashtag oligo (HTO) libraries were constructed using Chromium Single Cell 3? Feature Barcode Library Kit (both from 10X Genomics) at the Translational Science Laboratory (Medical University of South Carolina). Next generation sequencing was performed on each sample using an Illumina NovaSeq S4 flow cell at the VANTAGE facility (Vanderbilt University Medical Center).